LOCUS       sequence-334823-        5228 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Force-activating hairpin for 3'-to-5' helicase.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 5228)
  AUTHORS   Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT
  TITLE     Force-Activated DNA Substrates for In Situ Generation of ssDNA and 
            Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay.
  JOURNAL   Methods Mol Biol. 2022;2478:273-312. doi: 
            10.1007/978-1-0716-2229-2_10.
  PUBMED    36063324
REFERENCE   2  (bases 1 to 5228)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Dec 15, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "Methods Mol
            Biol."; date: "2022"; volume: "2478:273-312. doi"; pages: " 
            10.1007/978-1-0716-2229-2_10"
COMMENT     Sequence Label: hp-50%GC-Right-half-120bp
FEATURES             Location/Qualifiers
     source          1..5228
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     CDS             226..1416
                     /codon_start=1
                     /gene="tet"
                     /product="tetracycline efflux protein"
                     /label=TcR
                     /note="confers resistance to tetracycline"
                     /translation="MKSNNALIVILGTVTLDAVGIGLVMPVLPGLLRDIVHSDSIASHY
                     GVLLALYALMQFLCAPVLGALSDRFGRRPVLLASLLGATIDYAIMATTPVLWILYAGRI
                     VAGITGATGAVAGAYIADITDGEDRARHFGLMSACFGVGMVAGPVAGGLLGAISLHAPF
                     LAAAVLNGLNLLLGCFLMQESHKGERRPMPLRAFNPVSSFRWARGMTIVAALMTVFFIM
                     QLVGQVPAALWVIFGEDRFRWSATMIGLSLAVFGILHALAQAFVTGPATKRFGEKQAII
                     AGMAADALGYVLLAFATRGWIAFPIMILLASGGIGMPALQAMLSRQVDDDHQGQLQGSL
                     AALTSLTSIIGPLIVTAIYAASASTWNGLAWIVGAALYLVCLPALRRGAWSRATST"
     primer_bind     complement(578..597)
                     /label=pBRrevBam
                     /note="pBR322 vectors, tet region, downstream of BamHI, 
                     reverse primer"
     primer_bind     complement(1770..1789)
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        complement(1771..1789)
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(1796..1813)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(1796..1812)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1805..1827)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     CDS             1950..2252
                     /codon_start=1
                     /gene="ccdB"
                     /product="CcdB, a bacterial toxin that poisons DNA gyrase"
                     /label=ccdB
                     /note="Plasmids containing the ccdB gene cannot be 
                     propagated in standard E. coli strains."
                     /translation="QFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKV
                     SRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI"
     primer_bind     2131..2150
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
     CDS             2601..3395
                     /codon_start=1
                     /product="aminoglycoside phosphotransferase"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     CDS             2601..3395
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(2655..2674)
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     primer_bind     3265..3284
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     regulatory      3595..3604
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             3601..3975
                     /codon_start=1
                     /gene="Sh ble from Streptoalloteichus hindustanus"
                     /product="antibiotic-binding protein"
                     /label=BleoR
                     /note="confers resistance to bleomycin, phleomycin, and 
                     Zeocin(TM)"
                     /translation="MAKLTSAVPVLTARDVAGAVEFWTDRLGFSRDFVEDDFAGVVRDD
                     VTLFISAVQDQVVPDNTLAWVWVRGLDELYAEWSEVVSTNFRDASGPAMTEIGEQPWGR
                     EFALRDPAGNCVHFVAEEQD"
     rep_origin      4113..4701
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4602..4621
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     4855..4872
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    4989..5010
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(5025..5030,5031..5048,5049..5055)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    5063..5079
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     primer_bind     5068..5090
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     primer_bind     5087..5103
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     5087..5103
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
ORIGIN
        1 taaggatcca tttttatgga tccagacgtt gactcgtacg tcagtcgatc tagacgagca
       61 tgagctggtc gactctcatc aagagtgaca tcttgcttca ctgcttgact gtagctgcat
      121 acctgtgacc agagtcccgc tgtctagagg atccgactat cgacctcagc gctttaatgc
      181 ggtagtttat cacagttaaa ttgctaacgc agtcaggcac cgtgtatgaa atctaacaat
      241 gcgctcatcg tcatcctcgg caccgtcacc ctggatgctg taggcatagg cttggttatg
      301 ccggtactgc cgggcctctt gcgggatatc gtccattccg acagcatcgc cagtcactat
      361 ggcgtgctgc tagcgctata tgcgttgatg caatttctat gcgcacccgt tctcggagca
      421 ctgtccgacc gctttggccg ccgcccagtc ctgctcgctt cgctacttgg agccactatc
      481 gactacgcga tcatggcgac cacacccgtc ctgtggatcc tctacgccgg acgcatcgtg
      541 gccggcatca ccggcgccac aggtgcggtt gctggcgcct atatcgccga catcaccgat
      601 ggggaagatc gggctcgcca cttcgggctc atgagcgctt gtttcggcgt gggtatggtg
      661 gcaggccccg tggccggggg actgttgggc gccatctcct tgcatgcacc attccttgcg
      721 gcggcggtgc tcaacggcct caacctacta ctgggctgct tcctaatgca ggagtcgcat
      781 aagggagagc gtcgaccgat gcccttgaga gccttcaacc cagtcagctc cttccggtgg
      841 gcgcggggca tgactatcgt cgccgcactt atgactgtct tctttatcat gcaactcgta
      901 ggacaggtgc cggcagcgct ctgggtcatt ttcggcgagg accgctttcg ctggagcgcg
      961 acgatgatcg gcctgtcgct tgcggtattt ggaatcttgc acgccctcgc tcaagccttc
     1021 gtcactggtc ccgccaccaa acgtttcggc gagaagcagg ccattatcgc cggcatggcg
     1081 gccgacgcgc tgggctacgt cttgctggcg ttcgcgacgc gaggctggat agccttcccc
     1141 attatgattc ttctcgcttc cggcggcatc gggatgcccg cgttgcaggc catgctgtcc
     1201 aggcaggtag atgacgacca tcagggacag cttcaaggat cgctcgcggc tcttaccagc
     1261 ctaacttcga tcattggacc gctgatcgtc acggcgattt atgccgcctc ggcgagcaca
     1321 tggaacgggt tggcatggat tgtaggcgcc gccctatacc ttgtctgcct ccccgcgttg
     1381 cgtcgcggtg catggagccg ggccacctcg acctgaatgg aagccggcgg cacctcgcta
     1441 acggattcac cactccaaga attggagcca atcaattctt gcggagaact gtgaatgcgc
     1501 aaaccaaccc ttggcagaac atatccatcg cgtccgccat ctccagcagc cgcacgcggc
     1561 gcatctcggg cagcgttggg tcctggccac gggtgcgcat gatcatgctc ctgtcgttga
     1621 ggacccggct aggctggcgg ggttgcctta ctggttagca gaatgaatca ccgatacgcg
     1681 agcgaacgtg aagcgactgc aagggcgaat tctgcagata tccatcacac tggcggccgc
     1741 tcgagcatgc atctagaggg cccaattcgc cctatagtga gtcgtattac aattcactgg
     1801 ccgtcgtttt acaacgtcgt gactgggaaa accctggcgt tacccaactt aatcgccttg
     1861 cagcacatcc ccctttcgcc agctggcgta atagcgaaga ggcccgcacc gatcgccctt
     1921 cccaacagtt gcgcagccta tacgtacggc agtttaaggt ttacacctat aaaagagaga
     1981 gccgttatcg tctgtttgtg gatgtacaga gtgatattat tgacacgccg gggcgacgga
     2041 tggtgatccc cctggccagt gcacgtctgc tgtcagataa agtctcccgt gaactttacc
     2101 cggtggtgca tatcggggat gaaagctggc gcatgatgac caccgatatg gccagtgtgc
     2161 cggtctccgt tatcggggaa gaagtggctg atctcagcca ccgcgaaaat gacatcaaaa
     2221 acgccattaa cctgatgttc tggggaatat aaatgtcagg catgagatta tcaaaaagga
     2281 tcttcaccta gatccttttc acgtagaaag ccagtccgca gaaacggtgc tgaccccgga
     2341 tgaatgtcag ctactgggct atctggacaa gggaaaacgc aagcgcaaag agaaagcagg
     2401 tagcttgcag tgggcttaca tggcgatagc tagactgggc ggttttatgg acagcaagcg
     2461 aaccggaatt gccagctggg gcgccctctg gtaaggttgg gaagccctgc aaagtaaact
     2521 ggatggcttt cttgccgcca aggatctgat ggcgcagggg atcaagctct gatcaagaga
     2581 caggatgagg atcgtttcgc atgattgaac aagatggatt gcacgcaggt tctccggccg
     2641 cttgggtgga gaggctattc ggctatgact gggcacaaca gacaatcggc tgctctgatg
     2701 ccgccgtgtt ccggctgtca gcgcaggggc gcccggttct ttttgtcaag accgacctgt
     2761 ccggtgccct gaatgaactg caagacgagg cagcgcggct atcgtggctg gccacgacgg
     2821 gcgttccttg cgcagctgtg ctcgacgttg tcactgaagc gggaagggac tggctgctat
     2881 tgggcgaagt gccggggcag gatctcctgt catctcacct tgctcctgcc gagaaagtat
     2941 ccatcatggc tgatgcaatg cggcggctgc atacgcttga tccggctacc tgcccattcg
     3001 accaccaagc gaaacatcgc atcgagcgag cacgtactcg gatggaagcc ggtcttgtcg
     3061 atcaggatga tctggacgaa gagcatcagg ggctcgcgcc agccgaactg ttcgccaggc
     3121 tcaaggcgag catgcccgac ggcgaggatc tcgtcgtgac ccatggcgat gcctgcttgc
     3181 cgaatatcat ggtggaaaat ggccgctttt ctggattcat cgactgtggc cggctgggtg
     3241 tggcggaccg ctatcaggac atagcgttgg ctacccgtga tattgctgaa gagcttggcg
     3301 gcgaatgggc tgaccgcttc ctcgtgcttt acggtatcgc cgctcccgat tcgcagcgca
     3361 tcgccttcta tcgccttctt gacgagttct tctgaattat taacgcttac aatttcctga
     3421 tgcggtattt tctccttacg catctgtgcg gtatttcaca ccgcatcagg tggcactttt
     3481 cggggaaatg tgcgcggaac ccctatttgt ttatttttct aaatacattc aaatatgtat
     3541 ccgctcatga gacaataacc ctgataaatg cttcaataat agcacgtgag gagggccacc
     3601 atggccaagt tgaccagtgc cgttccggtg ctcaccgcgc gcgacgtcgc cggagcggtc
     3661 gagttctgga ccgaccggct cgggttctcc cgggacttcg tggaggacga cttcgccggt
     3721 gtggtccggg acgacgtgac cctgttcatc agcgcggtcc aggaccaggt ggtgccggac
     3781 aacaccctgg cctgggtgtg ggtgcgcggc ctggacgagc tgtacgccga gtggtcggag
     3841 gtcgtgtcca cgaacttccg ggacgcctcc gggccggcca tgaccgagat cggcgagcag
     3901 ccgtgggggc gggagttcgc cctgcgcgac ccggccggca actgcgtgca cttcgtggcc
     3961 gaggagcagg actgacacgt gctaaaactt catttttaat ttaaaaggat ctaggtgaag
     4021 atcctttttg ataatctcat gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg
     4081 tcagaccccg tagaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc
     4141 tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc ggatcaagag
     4201 ctaccaactc tttttccgaa ggtaactggc ttcagcagag cgcagatacc aaatactgtt
     4261 cttctagtgt agccgtagtt aggccaccac ttcaagaact ctgtagcacc gcctacatac
     4321 ctcgctctgc taatcctgtt accagtggct gctgccagtg gcgataagtc gtgtcttacc
     4381 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
     4441 tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata cctacagcgt
     4501 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaagc
     4561 ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt
     4621 tatagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg atgctcgtca
     4681 ggggggcgga gcctatggaa aaacgccagc aacgcggcct ttttacggtt cctggccttt
     4741 tgctggcctt ttgctcacat gttctttcct gcgttatccc ctgattctgt ggataaccgt
     4801 attaccgcct ttgagtgagc tgataccgct cgccgcagcc gaacgaccga gcgcagcgag
     4861 tcagtgagcg aggaagcgga agagcgccca atacgcaaac cgcctctccc cgcgcgttgg
     4921 ccgattcatt aatgcagctg gcacgacagg tttcccgact ggaaagcggg cagtgagcgc
     4981 aacgcaatta atgtgagtta gctcactcat taggcacccc aggctttaca ctttatgctt
     5041 ccggctcgta tgttgtgtgg aattgtgagc ggataacaat ttcacacagg aaacagctat
     5101 gaccatgatt acgccaagct atttaggtga cgcgttagaa tactcaagct atgcatcaag
     5161 cttggtaccg agctcggatc cactagtaac ggccgccagt gtgatggata tctgcagaat
     5221 tcgccctt
//
